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- PDB-2kcv: Solution nmr structure of tetratricopeptide repeat domain protein... -

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Basic information

Entry
Database: PDB / ID: 2kcv
TitleSolution nmr structure of tetratricopeptide repeat domain protein sru_0103 from salinibacter ruber, northeast structural genomics consortium (nesg) target srr115c
ComponentsTetratricopeptide repeat domain proteinTetratricopeptide repeat
Keywordsstructural genomics / unknown function / TETRATRICOPEPTIDE REPEAT / TPR / GFT NMR / RDC / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NUCLEOTIDE-BINDING PROTEIN
Function / homology
Function and homology information


Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Tetratricopeptide repeat domain protein
Similarity search - Component
Biological speciesSalinibacter ruber DSM 13855 (bacteria)
MethodSOLUTION NMR / distance geometry, torsion angle dynamics, simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsLiu, G. / Rossi, P. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. ...Liu, G. / Rossi, P. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution nmr structure of tetratricopeptide repeat domain protein sru_0103 from salinibacter ruber, northeast structural genomics consortium (nesg) target srr115c
Authors: Liu, G. / Montelione, G.T.
History
DepositionDec 29, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetratricopeptide repeat domain protein


Theoretical massNumber of molelcules
Total (without water)11,4871
Polymers11,4871
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Tetratricopeptide repeat domain protein / Tetratricopeptide repeat


Mass: 11487.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salinibacter ruber DSM 13855 (bacteria)
Gene: SRU_0103 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / References: UniProt: Q2S6C5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The structure was refined with RDC constraints in addition to NOE distance and dihedral angle constraints.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
2332D 1H-15N HSQC-TROSY
1413D 1H-15N NOESY
1513D 1H-13C NOESY aliphatic
1613D 1H-13C NOESY aromatic
1714,3D GFT CABCACONHN
1814,3D GFT HNNCABCA
1914,3D GFT HABCAB(CO)NHN
11013D (H)CCH-COSY
11122D 1H-15N HSQC
11222D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.37 mM [U-100% 13C; U-100% 15N] protein-1, 95% H2O/5% D2O95% H2O/5% D2O
21.05 mM [U-10% 13C; U-99% 15N] protein-2, 95% H2O/5% D2O95% H2O/5% D2O
31.09 mM [U-10% 13C; U-99% 15N] protein-3, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.37 mMprotein-1[U-100% 13C; U-100% 15N]1
1.05 mMprotein-2[U-10% 13C; U-99% 15N]2
1.09 mMprotein-3[U-10% 13C; U-99% 15N]3
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1n.a. 6.5 ambient atm298 K
2n.a. 6.5 ambient atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
AutoStructureHuang, Tejero, Powers and Montelionerefinement
AutoStructureHuang, Tejero, Powers and Montelionepeak picking
AutoStructureHuang, Tejero, Powers and Montelionedata analysis
PSVSBhattacharya and Montelionerefinement
PSVSBhattacharya and Montelionepeak picking
PSVSBhattacharya and Montelionedata analysis
XEASYBartels et al.refinement
XEASYBartels et al.peak picking
XEASYBartels et al.data analysis
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoAssignZimmerman, Moseley, Kulikowski and Montelionedata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
VnmrJVariancollection
RefinementMethod: distance geometry, torsion angle dynamics, simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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